I already did it, but it seems that it is not working. For example I added
several lines like this:
DIHE
> Ti6-Ot3-Ti6-Ot3 1 0.0 0.0 0.0
> Ti5-Ot2-Ti6-Ot2 1 0.0 0.0 0.0
> Ti5-Ot3-Ti5-Ot2 1 0.0 0.0 0.0
>
Ht1-Ot3-Ti6-Ot3 1 0.0 0.0 0.0
...
To cover all possible combinations. Still I get error message for the
torsions:
> ** No torsion terms for Ht1-Ot3-Ti6-Ot3
Even if the Ht1-Ot3-Ti6-Ot3 was included in the frcmod file under the DIHE
section.
Best,
Stefano
Il giorno gio 21 nov 2019 alle ore 13:01 Carlos Simmerling <
carlos.simmerling.gmail.com> ha scritto:
> I think you'll need to add the missing torsion parameters like you did with
> bond and angle. if you aren't concerned with specific values, generic ones
> may be easier (X-OT3-TI6-X etc)
> others on the list may know a better workaround...
>
> On Thu, Nov 21, 2019 at 6:28 AM Stefano Motta <stefano.motta.unimib.it>
> wrote:
>
> > I'm pretty sure it do not regard the prep and improper torsion (They are
> > for the organic molecules and I had used them with the non-bonded
> > forcefiled). Moreover I attach a leap.log for the NP only (without the
> > organic molecules). Still the same error.
> >
> > Thanks
> >
> > Stefano
> >
> > Il giorno gio 21 nov 2019 alle ore 12:22 Carlos Simmerling <
> > carlos.simmerling.gmail.com> ha scritto:
> >
> > > I'm not familiar with "prep-specified impropers", maybe others are... I
> > > speculate that your prep file lists improper torsions but you don't
> have
> > > parameters for them, maybe that's why it fails? does your prep file
> list
> > > improper torsions?
> > >
> > > On Thu, Nov 21, 2019 at 6:13 AM Stefano Motta <stefano.motta.unimib.it
> >
> > > wrote:
> > >
> > > > Still get error (Parameter file was not saved.) (Note that this time
> > you
> > > > don't have the angle warnings.
> > > >
> > > > Stefano
> > > >
> > > > Il giorno gio 21 nov 2019 alle ore 12:00 Carlos Simmerling <
> > > > carlos.simmerling.gmail.com> ha scritto:
> > > >
> > > > > If you include the angles and only get torsion warnings you should
> > > still
> > > > > generate the leap output files and be able to do md.
> > > > >
> > > > > On Thu, Nov 21, 2019, 5:49 AM Stefano Motta <
> stefano.motta.unimib.it
> > >
> > > > > wrote:
> > > > >
> > > > > > The only "warnings" that I have in the leap.log are a list of:
> > > > > >
> > > > > > Residue 0: DOC, Terminal/last, was not found in name map.
> > > > > >
> > > > > >
> > > > > > which I had also when I used a nonbonded version of the
> force-field
> > > for
> > > > > the
> > > > > > NP that worked. (DOC and DOD are organic molecules bound to the
> > NP).
> > > > > Then a
> > > > > > list of
> > > > > >
> > > > > > Could not find angle parameter: Ot3 - Ti6 - Ot3
> > > > > >
> > > > > >
> > > > > > for the angles, then a list of:
> > > > > >
> > > > > > 1-4: angle 551 586 duplicates bond ('triangular' bond) or angle
> > > > ('square'
> > > > > > > bond)
> > > > > >
> > > > > >
> > > > > > Which should be normal given the structure of the NP, then a list
> > of
> > > > > > different
> > > > > >
> > > > > > ** No torsion terms for Ht1-Ot3-Ti6-Ot3
> > > > > >
> > > > > >
> > > > > > For the dihedral. I can get rid of the angle warnings including
> > them
> > > in
> > > > > the
> > > > > > frcmod file, but even if I insert a line for Ht1-Ot3-Ti6-Ot3
> > torsion
> > > in
> > > > > the
> > > > > > frcmod, I still get the last torsion warning by tleap.
> > > > > >
> > > > > > I attach the complete leap.log file.
> > > > > >
> > > > > > Best
> > > > > > Stefano
> > > > > >
> > > > > >
> > > > > > Il giorno gio 21 nov 2019 alle ore 11:14 Carlos Simmerling <
> > > > > > carlos.simmerling.gmail.com> ha scritto:
> > > > > >
> > > > > > > For dihedrals you should not get errors, only warnings. Are you
> > > sure
> > > > > they
> > > > > > > are errors thet cause leap to stop?
> > > > > > >
> > > > > > > On Thu, Nov 21, 2019, 5:05 AM Stefano Motta <
> > > stefano.motta.unimib.it
> > > > >
> > > > > > > wrote:
> > > > > > >
> > > > > > > > Hello,
> > > > > > > >
> > > > > > > > I'm trying to use a force-field for TiO2, with only
> > > electrostatic,
> > > > > VdW,
> > > > > > > and
> > > > > > > > bond terms. I decided to create a mol2 file for the TiO2
> > > > nanoparticle
> > > > > > > (NP)
> > > > > > > > and treat the NP as a whole residue (the charges for the NP
> > atoms
> > > > are
> > > > > > in
> > > > > > > > the mol2 file with the connectivity). Then I created an
> frcmod
> > > that
> > > > > > > > contains the mass, bonded and VdW parameters.
> > > > > > > >
> > > > > > > > Anyway it seems that tleap is also searching for angle and
> > > dihedral
> > > > > > term
> > > > > > > > (that I don't want to include) and gives me error. Then I
> > > included
> > > > > the
> > > > > > > > ANGLE and DIHE terms (putting them to 0) in the frcmod (all
> the
> > > > > missing
> > > > > > > > parameters):
> > > > > > > > For example in case of angle, a lot of lines like this:
> > > > > > > > Ti6-Ot3-Ti6 0.0 0.0
> > > > > > > > and in case of dihedral, a lot of lines like this:
> > > > > > > > Ti6-Ot3-Ti6-Ot3 1 0.0 0.0 2.0
> > > > > > > >
> > > > > > > > Covering all the possible combinations of Angle and
> dihedrals.
> > > > > > > > This resolved the problem for angle (tleap is not complaining
> > > about
> > > > > > > missing
> > > > > > > > parameters for angles) but not for dihedrals (I still get
> > errors
> > > > even
> > > > > > for
> > > > > > > > dihedrals terms that I have inserted in the frcmod).
> > > > > > > >
> > > > > > > > How can I solve this issue? Is there a way to disable the
> > search
> > > > for
> > > > > > > angle
> > > > > > > > and dihedral terms for this molecule?
> > > > > > > >
> > > > > > > > Thanks in advance
> > > > > > > > Best,
> > > > > > > > Stefano
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > --
> > > > > > > >
> > ________________________________________________________________
> > > > > > > >
> > > > > > > > Stefano Motta PhD
> > > > > > > >
> > > > > > > > Email: stefano.motta.unimib.it <s.motta17.campus.unimib.it>
> > > > > > > > *Field of study:* Molecular Modeling, and Proteins Molecular
> > > > Dynamics
> > > > > > > >
> > > > > > > > Università degli Studi di Milano Bicocca
> > > > > > > > Department of Earth and Environmental Sciences
> > > > > > > >
> > > > > > > > Piazza dell'Ateneo Nuovo, 1 - 20126, Milano (Italy).
> > > > > > > >
> > _________________________________________________________________
> > > > > > > > _______________________________________________
> > > > > > > > AMBER mailing list
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> > > > > > > >
> > > > > > > _______________________________________________
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> > > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > ________________________________________________________________
> > > > > >
> > > > > > Stefano Motta PhD
> > > > > >
> > > > > > Email: stefano.motta.unimib.it <s.motta17.campus.unimib.it>
> > > > > > *Field of study:* Molecular Modeling, and Proteins Molecular
> > Dynamics
> > > > > >
> > > > > > Università degli Studi di Milano Bicocca
> > > > > > Department of Earth and Environmental Sciences
> > > > > >
> > > > > > Piazza dell'Ateneo Nuovo, 1 - 20126, Milano (Italy).
> > > > > > _________________________________________________________________
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
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> > > > > >
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> > > > >
> > > >
> > > >
> > > > --
> > > > ________________________________________________________________
> > > >
> > > > Stefano Motta PhD
> > > >
> > > > Email: stefano.motta.unimib.it <s.motta17.campus.unimib.it>
> > > > *Field of study:* Molecular Modeling, and Proteins Molecular Dynamics
> > > >
> > > > Università degli Studi di Milano Bicocca
> > > > Department of Earth and Environmental Sciences
> > > >
> > > > Piazza dell'Ateneo Nuovo, 1 - 20126, Milano (Italy).
> > > > _________________________________________________________________
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
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> > > >
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> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> > ________________________________________________________________
> >
> > Stefano Motta PhD
> >
> > Email: stefano.motta.unimib.it <s.motta17.campus.unimib.it>
> > *Field of study:* Molecular Modeling, and Proteins Molecular Dynamics
> >
> > Università degli Studi di Milano Bicocca
> > Department of Earth and Environmental Sciences
> >
> > Piazza dell'Ateneo Nuovo, 1 - 20126, Milano (Italy).
> > _________________________________________________________________
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
________________________________________________________________
Stefano Motta PhD
Email: stefano.motta.unimib.it <s.motta17.campus.unimib.it>
*Field of study:* Molecular Modeling, and Proteins Molecular Dynamics
Università degli Studi di Milano Bicocca
Department of Earth and Environmental Sciences
Piazza dell'Ateneo Nuovo, 1 - 20126, Milano (Italy).
_________________________________________________________________
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 21 2019 - 05:30:03 PST
